Bats, objectivity, and viral spillover risk.

What should the best practices be for modeling zoonotic disease risks, e.g. to anticipate the next pandemic, when background assumptions are unsettled or evolving rapidly? This challenge runs deeper than one might expect, all the way into how we model the robustness of contemporary phylogenetic inference and taxonomic classifications. Different and legitimate taxonomic assumptions can destabilize the putative objectivity of zoonotic risk assessments, thus potentially supporting inconsistent and overconfident policy decisions.

Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion.

Phylogenomic research is accelerating the publication of landmark studies that aim to resolve deep divergences of major organismal groups. Meanwhile, systems for identifying and integrating the products of phylogenomic inference-such as newly supported clade concepts-have not kept pace. However, the ability to verbalize node concept congruence and conflict across multiple, in effect simultaneously endorsed phylogenomic hypotheses, is a prerequisite for building synthetic data environments for biological systematics and other domains impacted by these conflicting inferences. Here we develop a novel solution to the conflict verbalization challenge, based on a logic representation and reasoning approach that utilizes the language of Region Connection Calculus (RCC-5) to produce consistent alignments of node concepts endorsed by incongruent phylogenomic studies. The approach employs clade concept labels to individuate concepts used by each source, even if these carry identical names. Indirect RCC-5 modeling of intensional (property-based) node concept definitions, facilitated by the local relaxation of coverage constraints, allows parent concepts to attain congruence in spite of their differentially sampled children. To demonstrate the feasibility of this approach, we align two recent phylogenomic reconstructions of higher-level avian groups that entail strong conflict in the "neoavian explosion" region. According to our representations, this conflict is constituted by 26 instances of input "whole concept" overlap. These instances are further resolvable in the output labeling schemes and visualizations as "split concepts", which provide the labels and relations needed to build truly synthetic phylogenomic data environments. Because the RCC-5 alignments fundamentally reflect the trained, logic-enabled judgments of systematic experts, future designs for such environments need to promote a culture where experts routinely assess the intensionalities of node concepts published by our peers-even and especially when we are not in agreement with each other.

Coordinating dissent as an alternative to consensus classification: insights from systematics for bio-ontologies.

The collection and classification of data into meaningful categories is a key step in the process of knowledge making. In the life sciences, the design of data discovery and integration tools has relied on the premise that a formal classificatory system for expressing a body of data should be grounded in consensus definitions for classifications. On this approach, exemplified by the realist program of the Open Biomedical Ontologies Foundry, progress is maximized by grounding the representation and aggregation of data on settled knowledge. We argue that historical practices in systematic biology provide an important and overlooked alternative approach to classifying and disseminating data, based on a principle of coordinative rather than definitional consensus. Systematists have developed a robust system for referring to taxonomic entities that can deliver high quality data discovery and integration without invoking consensus about reality or "settled" science.

Finding our way through phenotypes.

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.

A logic approach to modelling nomenclatural change.

We utilize an Answer Set Programming (ASP) approach to show that the principles of nomenclature are tractable in computational logic. To this end we design a hypothetical, 20 nomenclatural taxon use case, with starting conditions that embody several overarching principles of the International Code of Zoological Nomenclature, including Binomial Nomenclature, Priority, Coordination, Homonymy, Typification and the structural requirement of Gender Agreement. The use case ending conditions are triggered by the reinterpretation of the diagnostic features of one of 12 type specimens anchoring the corresponding species-level epithets. Permutations of this child-to-parent reassignment action lead to 36 alternative scenarios, where each scenario requires a set of 1-14 logically contingent nomenclatural emendations. We show that an ASP transition system approach can correctly infer the Code-mandated changes for each scenario, and visually output the ending conditions. The results provide a foundation for further developing logic-based nomenclatural change optimization and validation services, which could be applied in global nomenclatural registries. More generally, logic explorations of nomenclatural and taxonomic change scenarios provide a novel means of assessing design biases inherent in the principles of nomenclature, and can therefore inform the design of future, big data-compatible identifier systems that recognize and mitigate these constraints.

Model selection in statistical historical biogeography of Neotropical insects-The Exophthalmus genus complex (Curculionidae: Entiminae).

Statistical historical biogeographic methods rely on models that represent various biogeographic processes. Until recently model selection in this domain was not widely used, and the impact of differential model selection on inferring biogeographic scenarios was not well understood. Focusing on Neotropical weevils in the Exophthalmus genus complex (EGC) (Insecta: Curculionidae: Entiminae), we compare three commonly used biogeographic models - DIVA (Dispersal-Vicariance Analysis), DEC (Dispersal-Extinction-Cladogenesis) and BayArea (Bayesian Analysis of Biogeography), and examine the impact of modeling founder-event jump dispersal on historical biogeographic reconstructions. We also investigate the biogeographic events that have shaped patterns of distribution, diversification, and endemism in this weevil lineage. We sample representatives of 65 species of the EGC and 26 outgroup terminals from the Neotropics, including Caribbean islands and the mainland. We reconstruct a molecular phylogeny based on six genes and apply molecular dating using a relaxed clock with three fossil calibration points. Historical biogeographic estimations and alternative biogeographic models are computed and compared with the R package BioGeoBEARS. Model selection strongly favors biogeographic models that include founder-event jump dispersal. Without modeling jump dispersal, estimations based on the three biogeographic models are dramatically different, especially for early-diverging nodes. When jump dispersal is included, the three biogeographic models perform similarly. Accordingly, we show that the Neotropical mainland was colonized by Caribbean species in the early Miocene, and that in situ diversification accounts for a majority (∼75%) of the biogeographic events in the EGC. Our study highlights the need to assess wide-ranging historical biogeographic processes - including founder-event jump dispersal - for best-fitting statistical Caribbean biogeographic reconstructions. Moreover, colonization of the Neotropical mainland from the Caribbean reinforces the notion that islands can be an important source of continental diversity.

Two Influential Primate Classifications Logically Aligned.

Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence in ways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications. We demonstrate that such alignments are feasible for two classifications of primates corresponding to the second and third MSW editions. Our approach has three main components: (i) use of taxonomic concept labels, that is name sec. author (where sec. means according to), to assemble each concept hierarchy separately via parent/child relationships; (ii) articulation of select concepts across the two hierarchies with user-provided Region Connection Calculus (RCC-5) relationships; and (iii) the use of an Answer Set Programming toolkit to infer and visualize logically consistent alignments of these input constraints. Our use case entails the Primates sec. Groves (1993; MSW2-317 taxonomic concepts; 233 at the species level) and Primates sec. Groves (2005; MSW3-483 taxonomic concepts; 376 at the species level). Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every concept pair in the Primates sec. MSW2/MSW3. The complete alignment, and various partitions thereof, facilitate quantitative analyses of name:meaning dissociation, revealing that nearly one in three taxonomic names are not reliable across treatments-in the sense of the same name identifying congruent taxonomic meanings. The RCC-5 alignment approach is potentially widely applicable in systematics and can achieve scalable, precise resolution of semantically evolving name usages in synthetic, next-generation biodiversity, and phylogeny data platforms.

A multilayer micromechanical model of the cuticle of Curculio longinasus Chittenden, 1927 (Coleoptera: Curculionidae).

Curculio longinasus Chittenden, 1927 (Coleoptera: Curculionidae), is a weevil species common throughout the southwestern United States that uses its rostrum - a very slender, curved, beak-like projection of the head - to excavate tunnels in plant organs (such as acorns) for egg laying (oviposition). Once the apical portion of the rostrum has been inserted into the preferred substrate for oviposition, the female begins rotating around the perimeter of the hole, elevating her head by extending the fore-legs, and rotating the head in place in a drilling motion. This action causes significant elastic deformation of the rostrum, which will bend until it becomes completely straight. To better understand the mechanical behavior of the cuticle as it undergoes deformation during the preparation of oviposition sites, we develop a comprehensive micro/macro model of the micromechanical structure and properties of the cuticle, spanning across all cuticular regions, and reliably mirroring the resultant macroscale properties of the cuticle. Our modeling approach relies on the use of multi-scale, hierarchical biomaterial representation, and employs various micromechanical schemata - e.g., Mori-Tanaka, effective field, and Maxwell - to calculate the homogenized properties of representative volume elements at each level in the hierarchy. We describe the configuration and behavior of this model in detail, and discuss the theoretical implications and limitations of this approach with emphasis on future biomechanical and comparative evolutionary research. Our detailed account of this approach can thereby serve as a methodological template for exploring the biomechanical behavior of new insect structures.

Anatomy of a cladistic analysis.

The sequential stages culminating in the publication of a morphological cladistic analysis of weevils in the Exophthalmus genus complex (Coleoptera: Curculionidae: Entiminae) are reviewed, with an emphasis on how early-stage homology assessments were gradually evaluated and refined in light of intermittent phylogenetic insights. In all, 60 incremental versions of the evolving character matrix were congealed and analysed, starting with an assembly of 52 taxa and ten traditionally deployed diagnostic characters, and ending with 90 taxa and 143 characters that reflect significantly more narrow assessments of phylogenetic similarity and scope. Standard matrix properties and analytical tree statistics were traced throughout the analytical process, and series of incongruence length indifference tests were used to identify critical points of topology change among succeeding matrix versions. This kind of parsimony-contingent rescoping is generally representative of the inferential process of character individuation within individual and across multiple cladistic analyses. The expected long-term outcome is a maturing observational terminology in which precise inferences of homology are parsimony-contingent, and the notions of homology and parsimony are inextricably linked. This contingent view of cladistic character individuation is contrasted with current approaches to developing phenotype ontologies based on homology-neutral structural equivalence expressions. Recommendations are made to transparently embrace the parsimony-contingent nature of cladistic homology.

The Mosquito Fauna of Arizona: Species Composition and Public Health Implications.

Arizona is home to many mosquito species, some of which are known vectors of infectious diseases that harm both humans and animals. Here, we provide an overview of the 56 mosquito species that have been identified in the State to date, but also discuss their known feeding preference and the diseases they can (potentially) transmit to humans and animals. This list is unlikely to be complete for several reasons: (i) Arizona's mosquitoes are not systematically surveyed in many areas, (ii) surveillance efforts often target specific species of interest, and (iii) doubts have been raised by one or more scientists about the accuracy of some collection records, which has been noted in this article. There needs to be an integrated and multifaceted surveillance approach that involves entomologists and epidemiologists, but also social scientists, wildlife ecologists, ornithologists, representatives from the agricultural department, and irrigation and drainage districts. This will allow public health officials to (i) monitor changes in current mosquito species diversity and abundance, (ii) monitor the introduction of new or invasive species, (iii) identify locations or specific populations that are more at risk for mosquito-borne diseases, and (iv) effectively guide vector control.

Unified and pluralistic ideals for data sharing and reuse in biodiversity.

How should billions of species observations worldwide be shared and made reusable? Many biodiversity scientists assume the ideal solution is to standardize all datasets according to a single, universal classification and aggregate them into a centralized, global repository. This ideal has known practical and theoretical limitations, however, which justifies investigating alternatives. To support better community deliberation and normative evaluation, we develop a novel conceptual framework showing how different organizational models, regulative ideals and heuristic strategies are combined to form shared infrastructures supporting data reuse. The framework is anchored in a general definition of data pooling as an activity of making a taxonomically standardized body of information available for community reuse via digital infrastructure. We describe and illustrate unified and pluralistic ideals for biodiversity data pooling and show how communities may advance toward these ideals using different heuristic strategies. We present evidence for the strengths and limitations of the unification and pluralistic ideals based on systemic relationships of power, responsibility and benefit they establish among stakeholders, and we conclude the pluralistic ideal is better suited for biodiversity data.

Insect collecting bias in Arizona with a preliminary checklist of the beetles from the Sand Tank Mountains.

Background: The State of Arizona in the south-western United States supports a high diversity of insects. Digitised occurrence records, especially from preserved specimens in natural history collections, are an important and growing resource to understand biodiversity and biogeography. Underlying bias in how insects are collected and what that means for interpreting patterns of insect diversity is largely untested. To explore the effects of insect collecting bias in Arizona, the State was regionalised into specific areas. First, the entire State was divided into broad biogeographic areas by ecoregion. Second, the 81 tallest mountain ranges were mapped on to the State. The distribution of digitised records across these areas were then examined.A case study of surveying the beetles (Insecta, Coleoptera) of the Sand Tank Mountains is presented. The Sand Tanks are a low-elevation range in the Lower Colorado River Basin subregion of the Sonoran Desert from which a single beetle record was published before this study. New information: The number of occurrence records and collecting events are very unevenly distributed throughout Arizona and do not strongly correlate with the geographic size of areas. Species richness is estimated for regions in Arizona using rarefaction and extrapolation. Digitised records from the disproportionately highly collected areas in Arizona represent at best 70% the total insect diversity within them. We report a total of 141 species of Coleoptera from the Sand Tank Mountains, based on 914 digitised voucher specimens. These specimens add important new records for taxa that were previously unavailable in digitised data and highlight important biogeographic ranges.Possible underlying mechanisms causing bias are discussed and recommendations are made for future targeted collecting of under-sampled regions. Insect species diversity is apparently at best 70% documented for the State of Arizona with many thousands of species not yet recorded. The Chiricahua Mountains are the most densely sampled region of Arizona and likely contain at least 2,000 species not yet vouchered in online data. Preliminary estimates for species richness of Arizona are at least 21,000 and likely much higher. Limitations to analyses are discussed which highlight the strong need for more insect occurrence data.

A globally integrated structure of taxonomy to support biodiversity science and conservation.

All aspects of biodiversity research, from taxonomy to conservation, rely on data associated with species names. Effective integration of names across multiple fields is paramount and depends on the coordination and organization of taxonomic data. We assess current efforts and find that even key applications for well-studied taxa still lack commonality in taxonomic information required for integration. We identify essential taxonomic elements from our interoperability assessment to support improved access and integration of taxonomic data. A stronger focus on these elements has the potential to involve taxonomic communities in biodiversity science and overcome broken linkages currently limiting research capacity. We encourage a community effort to democratize taxonomic expertise and language in order to facilitate maximum interoperability and integration.

Wanted: Standards for FAIR taxonomic concept representations and relationships.

Making the most of biodiversity data requires linking observations of biological species from multiple sources both efficiently and accurately (Bisby 2000, Franz et al. 2016). Aggregating occurrence records using taxonomic names and synonyms is computationally efficient but known to experience significant limitations on accuracy when the assumption of one-to-one relationships between names and biological entities breaks down (Remsen 2016, Franz and Sterner 2018). Taxonomic treatments and checklists provide authoritative information about the correct usage of names for species, including operational representations of the meanings of those names in the form of range maps, reference genetic sequences, or diagnostic traits. They increasingly provide taxonomic intelligence in the form of precise description of the semantic relationships between different published names in the literature. Making this authoritative information Findable, Accessible, Interoperable, and Reusable (FAIR; Wilkinson et al. 2016) would be a transformative advance for biodiversity data sharing and help drive adoption and novel extensions of existing standards such as the Taxonomic Concept Schema and the OpenBiodiv Ontology (Kennedy et al. 2006, Senderov et al. 2018). We call for the greater, global Biodiversity Information Standards (TDWG) and taxonomy community to commit to extending and expanding on how FAIR applies to biodiversity data and include practical targets and criteria for the publication and digitization of taxonomic concept representations and alignments in taxonomic treatments, checklists, and backbones.

Reducing the risk of rostral bending failure in Curculio Linnaeus, 1758.

With over 300 species worldwide, the genus Curculio Linnaeus, 1758 is a widespread, morphologically diverse lineage of weevils that mainly parasitize nuts. Females use the rostrum, an elongate cuticular extension of the head, to excavate oviposition sites. This process causes extreme bending and deformation of the rostrum, without apparent harm to the structure. The cuticle of the rostral apex exhibits substantial modifications to its composite structure that enhance the elasticity and resiliency of this structure. Here we develop finite element models of the head and rostrum for three Curculio species representing disparate North American clades and rostral morphotypes. The models were subjected to varying apical loads and to prescribed dislocation of the head capsule, with and without representing the cuticular modifications of the rostral apex. We found that the altered layer thicknesses and macrofiber orientation angles of the rostral apex fully explain the observed elasticity of the rostrum. These modifications have a synergistic effect that greatly enhances the flexibility of the rostral apex. Consequently, the cuticle composite profile of the rostral apex substantially mitigates the risk of fracture in dorso-apical flexion. Removing the cuticular modifications, in turn, causes a negative margin of safety for rostral bending, implying strong risk of catastrophic structural failure. The occipital sulci were identified as an important source of biomechanical constraint upon the elasticity of the rostrum, and exhibit the greatest risk of failure within this structure. The apical cuticle profile greatly reduced the maximum stresses and strain energy accumulated in the rostrum, thereby resulting in a positive margin of safety and reducing the risk of fracture. Our findings imply that the primary selective pressure influencing the evolution of the rostral cuticle was most likely negative selection of structural failure caused by bending. STATEMENT OF SIGNIFICANCE: Weevils are among the most diverse and evolutionarily successful animal lineages on Earth. Their success is driven in part by a structure called the rostrum, which gives weevil heads a characteristic "snout-like" appearance. Nut weevils in the genus Curculio use the rostrum to drill holes into developing fruits and nuts, into which they deposit their eggs. During oviposition this exceedingly slender structure is bent into a straightened configuration - in some species up to 90∘ - but does not suffer any damage during this process. Using finite element models of the rostra of three morphologically distinct species, we show that the Curculio rostrum is only able to withstand repeated, extreme bending because of modifications to the composite structure of the cuticle in the rostral apex. These modifications were shown previously to enhance the intrinsic toughness of the cuticle; in this study, we demonstrate that modification of the rostral cuticle also results in more evenly distributed bending stresses, further reducing the risk of fracture. This is the first time that the laminate profile, orthotropic behavior, and functional gradation of the cuticle have been incorporated into a three-dimensional finite element model of an insect cuticular structure. Our models highlight the significance of biomechanical constraint - i.e., avoidance of catastrophic structural failure - on the evolution of insect morphology.

Liberating host-virus knowledge from biological dark data.

Connecting basic data about bats and other potential hosts of SARS-CoV-2 with their ecological context is crucial to the understanding of the emergence and spread of the virus. However, when lockdowns in many countries started in March, 2020, the world's bat experts were locked out of their research laboratories, which in turn impeded access to large volumes of offline ecological and taxonomic data. Pandemic lockdowns have brought to attention the long-standing problem of so-called biological dark data: data that are published, but disconnected from digital knowledge resources and thus unavailable for high-throughput analysis. Knowledge of host-to-virus ecological interactions will be biased until this challenge is addressed. In this Viewpoint, we outline two viable solutions: first, in the short term, to interconnect published data about host organisms, viruses, and other pathogens; and second, to shift the publishing framework beyond unstructured text (the so-called PDF prison) to labelled networks of digital knowledge. As the indexing system for biodiversity data, biological taxonomy is foundational to both solutions. Building digitally connected knowledge graphs of host-pathogen interactions will establish the agility needed to quickly identify reservoir hosts of novel zoonoses, allow for more robust predictions of emergence, and thereby strengthen human and planetary health systems.

Decentralized but Globally Coordinated Biodiversity Data.

Centralized biodiversity data aggregation is too often failing societal needs due to pervasive and systemic data quality deficiencies. We argue for a novel approach that embodies the spirit of the Web ("small pieces loosely joined") through the decentralized coordination of data across scientific languages and communities. The upfront cost of decentralization can be offset by the long-term benefit of achieving sustained expert engagement, higher-quality data products, and ultimately more societal impact for biodiversity data. Our decentralized approach encourages the emergence and evolution of multiple self-identifying communities of practice that are regionally, taxonomically, or institutionally localized. Each community is empowered to control the social and informational design and versioning of their local data infrastructures and signals. With no single aggregator to exert centralized control over biodiversity data, decentralization generates loosely connected networks of mid-level aggregators. Global coordination is nevertheless feasible through automatable data sharing agreements that enable efficient propagation and translation of biodiversity data across communities. The decentralized model also poses novel integration challenges, among which the explicit and continuous articulation of conflicting systematic classifications and phylogenies remain the most challenging. We discuss the development of available solutions, challenges, and outline next steps: the global effort of coordination should focus on developing shared languages for data signal translation, as opposed to homogenizing the data signal itself.

Avoidance of Catastrophic Structural Failure as an Evolutionary Constraint: Biomechanics of the Acorn Weevil Rostrum.

The acorn weevil (Curculio Linnaeus, 1758) rostrum (snout) exhibits remarkable flexibility and toughness derived from the microarchitecture of its exoskeleton. Modifications to the composite profile of the rostral cuticle that simultaneously enhance the flexibility and toughness of the distal portion of the snout are characterized. Using classical laminate plate theory, the effect of these modifications on the elastic behavior of the exoskeleton is estimated. It is shown that the tensile behavior of the rostrum across six Curculio species with high morphological variation correlates with changes in the relative layer thicknesses and orientation angles of layers in the exoskeleton. Accordingly, increased endocuticle thickness is strongly correlated with increased tensile strength. Rostrum stiffness is shown to be inversely correlated with work of fracture; thus allowing a highly curved rostrum to completely straighten without structural damage. Finally, exocuticle rich invaginations of the occipital sutures are identified both as a likely site of crack initiation in tensile failure and as a source of morphological constraint on the evolution of the rostrum in Curculio weevils. It is concluded that avoidance of catastrophic structural failure, as initiated in these sutures under tension, is the driving selective pressure in the evolution of the female Curculio rostrum.

To increase trust, change the social design behind aggregated biodiversity data.

Growing concerns about the quality of aggregated biodiversity data are lowering trust in large-scale data networks. Aggregators frequently respond to quality concerns by recommending that biologists work with original data providers to correct errors 'at the source.' We show that this strategy falls systematically short of a full diagnosis of the underlying causes of distrust. In particular, trust in an aggregator is not just a feature of the data signal quality provided by the sources to the aggregator, but also a consequence of the social design of the aggregation process and the resulting power balance between individual data contributors and aggregators. The latter have created an accountability gap by downplaying the authorship and significance of the taxonomic hierarchies-frequently called 'backbones'-they generate, and which are in effect novel classification theories that operate at the core of data-structuring process. The Darwin Core standard for sharing occurrence records plays an under-appreciated role in maintaining the accountability gap, because this standard lacks the syntactic structure needed to preserve the taxonomic coherence of data packages submitted for aggregation, potentially leading to inferences that no individual source would support. Since high-quality data packages can mirror competing and conflicting classifications, i.e. unsettled systematic research, this plurality must be accommodated in the design of biodiversity data integration. Looking forward, a key directive is to develop new technical pathways and social incentives for experts to contribute directly to the validation of taxonomically coherent data packages as part of a greater, trustworthy aggregation process.